NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|767906034|ref|XP_011540450|]
View 

protein lin-28 homolog A isoform X1 [Homo sapiens]

Protein Classification

cold shock domain-containing protein; S1 domain-containing protein( domain architecture ID 13626161)

cold shock domain-containing protein similar to mammalian Y-box-binding proteins, which are DNA- and RNA-binding proteins involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation| S1 domain-containing protein may bind RNA

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
42-112 7.83e-19

'Cold-shock' DNA-binding domain;


:

Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 7.83e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767906034   42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGP 112
Cdd:pfam00313   3 GTVKWFNAKKGFGFITPE-------DGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
AIR1 super family cl34894
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 120-183 1.27e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


The actual alignment was detected with superfamily member COG5082:

Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 38.29  E-value: 1.27e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767906034 120 SERRPKGKSMQKRRSKgdRCYNCGGLDHHAKEC--------------KLP-PQPKKCHFCQSISHMVASCPLKAQQGPS 183
Cdd:COG5082   46 EDRSVEDVSAIREENP--VCFNCGQNGHLRRDCphsicyncswdghrSNHcPKPKKCYNCGETGHLSRDCNPSKDQQKS 122
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
42-112 7.83e-19

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 7.83e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767906034   42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGP 112
Cdd:pfam00313   3 GTVKWFNAKKGFGFITPE-------DGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 42-111 9.87e-19

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 76.46  E-value: 9.87e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767906034  42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTG 111
Cdd:cd04458    3 GTVKWFDDEKGFGFITPD-------DGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
42-110 6.20e-14

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 64.06  E-value: 6.20e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767906034  42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVT 110
Cdd:COG1278    4 GTVKWFNAEKGFGFITPD-------DGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
42-110 1.59e-12

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 60.37  E-value: 1.59e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767906034  42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVT 110
Cdd:PRK10354   7 GIVKWFNADKGFGFITPD-------DGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT 68
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 42-112 4.88e-08

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 47.98  E-value: 4.88e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767906034    42 GICKWFNvrMGFGFLSMtaragvaLDPPVDVFVHQSKLHMeGFRSLKEGEAVEF--TFKKSAKGLESIRVTGP 112
Cdd:smart00357   2 GVVKWFN--KGFGFIRP-------DDGGKDVFVHPSQIQG-GLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 120-183 1.27e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 38.29  E-value: 1.27e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767906034 120 SERRPKGKSMQKRRSKgdRCYNCGGLDHHAKEC--------------KLP-PQPKKCHFCQSISHMVASCPLKAQQGPS 183
Cdd:COG5082   46 EDRSVEDVSAIREENP--VCFNCGQNGHLRRDCphsicyncswdghrSNHcPKPKKCYNCGETGHLSRDCNPSKDQQKS 122
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 134-190 1.59e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.48  E-value: 1.59e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767906034 134 SKGDRCYNCGGLDHHAKECKLPPQ----PKKCHFCQSISHMVASCPlkAQQGPSAQGKPTY 190
Cdd:PTZ00368  75 SGPRSCYNCGQTGHISRECPNRAKggaaRRACYNCGGEGHISRDCP--NAGKRPGGDKTCY 133
 
Name Accession Description Interval E-value
CSD pfam00313
'Cold-shock' DNA-binding domain;
42-112 7.83e-19

'Cold-shock' DNA-binding domain;


Pssm-ID: 278729  Cd Length: 66  Bit Score: 76.90  E-value: 7.83e-19
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767906034   42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTGP 112
Cdd:pfam00313   3 GTVKWFNAKKGFGFITPE-------DGDKDVFVHFSAIQGDGFRSLQEGQKVEFEVVEGTKGPQAANVTKP 66
CSP_CDS cd04458
Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in ...
 42-111 9.87e-19

Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea. CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA. CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.


Pssm-ID: 239905  Cd Length: 65  Bit Score: 76.46  E-value: 9.87e-19
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767906034  42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVTG 111
Cdd:cd04458    3 GTVKWFDDEKGFGFITPD-------DGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKGPQAVNVRL 65
CspC COG1278
Cold shock protein, CspA family [Transcription];
42-110 6.20e-14

Cold shock protein, CspA family [Transcription];


Pssm-ID: 440889  Cd Length: 67  Bit Score: 64.06  E-value: 6.20e-14
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767906034  42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVT 110
Cdd:COG1278    4 GTVKWFNAEKGFGFITPD-------DGGEDVFVHISALQRSGFRTLREGQRVEFEVEQGDKGPQAVNVR 65
PRK10354 PRK10354
RNA chaperone/antiterminator CspA;
42-110 1.59e-12

RNA chaperone/antiterminator CspA;


Pssm-ID: 182402  Cd Length: 70  Bit Score: 60.37  E-value: 1.59e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767906034  42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVT 110
Cdd:PRK10354   7 GIVKWFNADKGFGFITPD-------DGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKGPAAGNVT 68
cspE PRK09507
cold shock-like protein CspE;
42-110 1.40e-11

cold shock-like protein CspE;


Pssm-ID: 169931  Cd Length: 69  Bit Score: 57.74  E-value: 1.40e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767906034  42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVT 110
Cdd:PRK09507   6 GNVKWFNESKGFGFITPE-------DGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKGPSAANVI 67
PRK10943 PRK10943
cold shock-like protein CspC; Provisional
 42-110 3.23e-09

cold shock-like protein CspC; Provisional


Pssm-ID: 170841  Cd Length: 69  Bit Score: 51.61  E-value: 3.23e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767906034  42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKGLESIRVT 110
Cdd:PRK10943   6 GQVKWFNESKGFGFITPA-------DGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKGPAAVNVT 67
PRK09937 PRK09937
cold shock-like protein CspD;
42-103 1.92e-08

cold shock-like protein CspD;


Pssm-ID: 77494  Cd Length: 74  Bit Score: 49.73  E-value: 1.92e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767906034  42 GICKWFNVRMGFGFLSMTARAGvaldppvDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKG 103
Cdd:PRK09937   4 GTVKWFNNAKGFGFICPEGGGE-------DIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG 58
PRK09890 PRK09890
cold shock protein CspG; Provisional
 42-103 3.90e-08

cold shock protein CspG; Provisional


Pssm-ID: 77467  Cd Length: 70  Bit Score: 48.61  E-value: 3.90e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767906034  42 GICKWFNVRMGFGFLSMTaragvalDPPVDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKG 103
Cdd:PRK09890   7 GLVKWFNADKGFGFITPD-------DGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG 61
CSP smart00357
Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria ...
 42-112 4.88e-08

Cold shock protein domain; RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.


Pssm-ID: 214633 [Multi-domain]  Cd Length: 64  Bit Score: 47.98  E-value: 4.88e-08
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767906034    42 GICKWFNvrMGFGFLSMtaragvaLDPPVDVFVHQSKLHMeGFRSLKEGEAVEF--TFKKSAKGLESIRVTGP 112
Cdd:smart00357   2 GVVKWFN--KGFGFIRP-------DDGGKDVFVHPSQIQG-GLKSLREGDEVEFkvVSPEGGEKPEAENVVKL 64
PRK14998 PRK14998
cold shock-like protein CspD; Provisional
 42-103 6.89e-08

cold shock-like protein CspD; Provisional


Pssm-ID: 184960  Cd Length: 73  Bit Score: 48.12  E-value: 6.89e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 767906034  42 GICKWFNVRMGFGFLSMTARAGvaldppvDVFVHQSKLHMEGFRSLKEGEAVEFTFKKSAKG 103
Cdd:PRK14998   4 GTVKWFNNAKGFGFICPEGGGE-------DIFAHYSTIQMDGYRTLKAGQSVRFDVHQGPKG 58
AIR1 COG5082
Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational ...
 120-183 1.27e-03

Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion];


Pssm-ID: 227414 [Multi-domain]  Cd Length: 190  Bit Score: 38.29  E-value: 1.27e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 767906034 120 SERRPKGKSMQKRRSKgdRCYNCGGLDHHAKEC--------------KLP-PQPKKCHFCQSISHMVASCPLKAQQGPS 183
Cdd:COG5082   46 EDRSVEDVSAIREENP--VCFNCGQNGHLRRDCphsicyncswdghrSNHcPKPKKCYNCGETGHLSRDCNPSKDQQKS 122
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 134-190 1.59e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 37.48  E-value: 1.59e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767906034 134 SKGDRCYNCGGLDHHAKECKLPPQ----PKKCHFCQSISHMVASCPlkAQQGPSAQGKPTY 190
Cdd:PTZ00368  75 SGPRSCYNCGQTGHISRECPNRAKggaaRRACYNCGGEGHISRDCP--NAGKRPGGDKTCY 133
PTZ00368 PTZ00368
universal minicircle sequence binding protein (UMSBP); Provisional
 139-177 6.44e-03

universal minicircle sequence binding protein (UMSBP); Provisional


Pssm-ID: 173561 [Multi-domain]  Cd Length: 148  Bit Score: 35.94  E-value: 6.44e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|...
gi 767906034 139 CYNCGGLDHHAKEC----KLPPQPKKCHFCQSISHMVASCPLK 177
Cdd:PTZ00368 106 CYNCGGEGHISRDCpnagKRPGGDKTCYNCGQTGHLSRDCPDK 148
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH